Question

A protease is an enzyme that catalyzes the hydrolysis of the peptide bonds of target proteins. How might a protease bind a target protein so that its main chain becomes fully extended in the vicinity of the vulnerable peptide bond?

The hint that we got was this: look for a way the protease might stabilize the substrate during hydrolysis

I'm open to several possibilities at this point but please explain your answer in detail.

Answer 1

A segment of the main chain of the protease could hydrogen bond to the main chain of the substrate to form an extended parallel or antiparallel pair of ? strands.

Proteasomes: Selective protein degradation occurs in the proteasome, a large protein complex located in the nucleus and cytosol of eukaryotic cells. The proteasome core complex, which has a sedimentation coefficient of 20S, contains 2 copies each of 14 different polypeptides. 7 a-type proteins form each of the two a rings, at the ends of the cylindrical structure. 7 b-type proteins form each of the two central b rings. The 20S proteasome core complex encloses a cavity consisting of 3 compartments joined by narrow passageways. See diagrams p. 1360, 1362.

Protease activities are associated with three of the b subunits, each having different substrate specificity:

• One catalytic b subunit has a chymotrypsin-like activity with preference for tyrosine or phenylalanine at the P1 (peptide cabonyl) position.
• One has a trypsin-like activity with preference for arginine or lysine at the P1 position.
• One has a post-glutamyl activity with preference for glutamate or other acidic residue at the P1 position.

Different variants of the three catalytic subunits, with different substrate specificity, are produced in cells of the immune system that cleave proteins for antigen display.

The proteasome hydrolases constitute a unique family of threonine proteases. A conserved N-terminal threonine is involved in catalysis at each active site. The three catalytic b subunits are synthesized as pre-proteins. They are activated when the N-terminus is cleaved off, making threonine the N-terminal residue. Catalytic threonines are exposed at the lumenal surface.

Proteasomal degradation of particular proteins is an essential mechanism by which cellular processes are regulated, such as cell division, apoptosis, differentiation and development. For example, progression through the cell cycle is controlled in part through regulated degradation of proteins called cyclins that activate cyclin-dependent kinases.

Many inhibitors of proteasome protease activity are known, some of which are natural products and others experimentally produced. E.g., TMCs are naturally occurring proteasome inhibitors. They bind with high affinity adjacent to active site threonines within the proteasome core complex. TMCs have a heterocyclic ring structure derived from modified amino acids.

Proteasome inhibitors cause cell cycle arrest and induction of apoptosis (programmed cell death) when added to rapidly dividing cells. The potential use of proteasome inhibitors in treating cancer is being investigated.

Several subunits of the proteasome are glycosylated with GlcNAc (N-acetylglucosamine) when extracellular glucose is high, leading to decreased intracellular proteolysis. Conversely, under conditions of low nutrition, decreased modification by GlcNAc leads to increased proteolysis. Thus protein degradation is responsive to nutrition via glycosylation of both Ubiquitin Ligase (see above) and the proteasome itself.

Proteasome evolution: Proteasomes are considered very old. They are in archaebacteria, but not most eubacteria, although eubacteria have alternative protein-degrading complexes. The archaebacterial proteasome has just two protein types, a and b, with 14 copies of each. The eukaryotic proteasome has evolved 14 distinct proteins that occupy unique positions within the proteasome (7 a-type and 7 b-type). Explore at right the structure of the yeast 20S proteasome core complex.